[there are still many sites that] require third-party products such as Flash to work
I think this point should be looked at from the other side of the fence. Flash is not going away. It’s way way too popular and useful for too many websites.
Once you think of it like this, the problem becomes how tough it is to use Flash in a way that doesn’t invalidate your documents, which is where I think much more fucus needs to go these days.
Standardize the browser plugin architecture and I bet you’ll see way more XHTML valid Flash websites.